Mapping 70S ribosomes in intact cells by cryoelectron tomography and pattern recognition

Journal of Structural Biology

Volumn 156, Issue 2, 2006, Pages 334-341

  Ortiz, Julio O ^a   Förster, Friedrich ^a   Kürner, Julia ^a   Linaroudis, Alexandros A ^a   Baumeister, Wolfgang ^a  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

Cryoelectron tomography; Ribosome cellular distribution; Scaling index based segmentation; Spiroplasma melliferum; Template matching

Indexed keywords

AMPLIFIER; ANALYTIC METHOD; ARTICLE; CELL MEMBRANE; CELL STRUCTURE; COMPLEX FORMATION; CONTROLLED STUDY; CRYOELECTRON MICROSCOPY; CYTOLOGY; CYTOSOL; EXPERIMENTATION; IMAGE QUALITY; MACROMOLECULE; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; RIBOSOME; SIGNAL NOISE RATIO; SPIROPLASMA; STRUCTURE ANALYSIS; TOMOGRAPHY; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; CRYOELECTRON MICROSCOPY; CRYSTALLOGRAPHY, X-RAY; FEASIBILITY STUDIES; IMAGING, THREE-DIMENSIONAL; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; RIBOSOMES; SPIROPLASMA; TOMOGRAPHY, X-RAY COMPUTED;

PROKARYOTA; SPIROPLASMA MELLIFERUM;

EID: 33750527990     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2006.04.014     Document Type: Article

References (32)

1. Alberts B. The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92 (1998) 291-294
2. Asai T., Condon C., Voulgaris J., Zaporojets D., Shen B., Al-Omar M., Squires C., and Squires C.L. Construction and initial characterisation of Escherichia coli strains with few or no intact chromosomal rRNA operons. J. Bacteriol. 181 (1999) 3803-3809
3. Ban N., Nissen P., Hansen J., Moore P.B., and Steitz T.A. The complete atomic structure of the large ribosomal subunit at 2.4 angstrom resolution. Science 289 (2000) 905-920
4. Beck M., Forster F., Ecke M., Plitzko J.M., Melchior F., Gerisch G., Baumeister W., and Medalia O. Nuclear pore complex structure and dynamics revealed by cryoelectron tomography. Science 306 (2004) 1387-1390
5. Böhm J., Frangakis A.S., Hegerl R., Nickell S., Typke D., and Baumeister W. Toward detecting and identifying macromolecules in a cellular context: template matching applied to electron tomograms. Proc. Natl. Acad. Sci. USA 97 (2000) 14245-14250
6. Bremer H., and Dennis P.D. Modulation of chemical composition and other parameters of the cell by growth rate. In: Neidhardt F.C., Ingraham J.L., Low K.B., Megasanik B., Schaecter M., and Umbarger H.E. (Eds). Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology vol. 2 (1996), American Society for Microbiology Press, Washington, DC 1458-1496
7. Dubochet J., Adrian M., Chang J.J., Homo J.C., Lepault J., McDowall A.W., and Schultz P. Cryo-electron microscopy of vitrified specimens. Q. Rev. Biophys. 21 (1988) 129-228
8. Forchhammer J., and Lindahl L. Growth rate of polypeptide chains as a function of the cell growth rate in a mutant of Escherichia coli 15. J. Mol. Biol. 55 (1971) 563-568
9. Förster F., Medalia O., Zauberman N., Baumeister W., and Fass D. Retrovirus envelope protein complex structure in situ studied by cryo-electron tomography. Proc. Natl. Acad. Sci. USA 102 (2005) 4729-4734
10. Frangakis A.S., Bohm J., Forster F., Nickell S., Nicastro D., Typke D., Hegerl R., and Baumeister W. Identification of macromolecular complexes in cryoelectron tomograms of phantom cells. Proc. Natl. Acad. Sci. USA 99 (2002) 14153-14158
11. Frangakis A.S., and Hegerl R. Noise reduction in electron tomographic reconstructions using nonlinear anisotropic diffusion. J. Struct. Biol. 135 (2001) 239-250
12. Gabashvili I.S., Agrawal R.K., Spahn C.M.T., Grassucci R.A., Svergun D.I., Frank J., and Penczek P. Solution structure of the E. coli 70S ribosome at 11.5 angstrom resolution. Cell 100 (2000) 537-549
13. Grünewald K., Desai P., Winkler D.C., Heymann J.B., Belnap D.M., Baumeister W., and Steven A.C. Three-dimensional structure of herpes simplex virus from cryo-electron tomography. Science 302 (2003) 1396-1398
14. Harms J., Schluenzen F., Zarivach R., Bashan A., Gat S., Agmon I., Bartels H., Franceschi F., and Yonath A. High resolution structure of the large ribosomal subunit from a mesophilic Eubacterium. Cell 107 (2001) 679-688
15. Hegerl R. The EM program package: a platform for image processing in biological electron microscopy. J. Struct. Biol. 116 (1996) 30-34
16. Jamitzky F., Stark R.W., Bunk W., Thalhammer S., Rath C., Aschenbrenner T., Morfill G.E., and Heckl W.M. Scaling-index method as an image processing tool in scanning-probe microscopy. Ultramicroscopy 86 (2001) 241-246
17. Kürner J., Frangakis A.S., and Baumeister W. Cryo-electron tomography reveals the cytoskeletal structure of Spiroplasma melliferum. Science 307 (2005) 436-438
18. Lewis P.J., Thaker S.D., and Errington J. Compartmentalization of transcription and translation in Bacillus subtilis. EMBO J. 19 (2000) 710-718
19. Linaroudis, A., Hegerl, R., 2004. Automatic segmentation of electron tomograms by using the scaling index method. In: Dirk Van Dyck, Oostveldt, P.V. (Eds.), Proc. 13th European Microscopy Congress. Belgian Society for Microscopy, Antwerp, Belgium, vol. I, pp. 425-426.
20. Lučić V., Förster F., and Baumeister W. Structural studies by electron tomography: from cells to molecules. Annu. Rev. Biochem. 74 (2005) 833-865
21. Mascarenhas J., Weber M.H.W., and Graumann P.L. Specific polar localization of ribosomes in Bacillus subtilis depends on active transcription. EMBO Rep. 2 (2001) 685-689
22. Medalia O., Weber I., Frangakis A.S., Nicastro D., Gerisch G., and Baumeister W. Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography. Science 298 (2002) 1209-1213
23. Mitra K., Schaffitzel C., Shaikh T., Tama F., Jenni S., Brooks III C.L., Ban N., and Frank J. Structure of the E. coli protein-conducting channel bound to a translating ribosome. Nature 438 (2005) 318-324
24. Nickell S., Forster F., Linaroudis A., Del Net W., Beek F., Hegerl R., Baumeister W., and Plitzko J.M. TOM software toolbox: acquisition and analysis for electron tomography. J. Struct. Biol. 149 (2005) 227-234
25. Nickell S., Kofler C., Leis A.P., and Baumeister W. A visual approach to proteomics. Nat. Rev. Mol. Cell Biol. 7 (2006) 225-230
26. Roseman A.M. Particle finding in electron micrographs using a fast local correlation algorithm. Ultramicroscopy 94 (2003) 225-236
27. Schaevitz J.W., Lee J.Y., and Fletcher D.A. Spiroplasma swim by a processive change in body helicity. Cell 122 (2005) 941-945
28. Schluenzen F., Tocilj A., Zarivach R., Harms J., Gluehmann M., Janell D., Bashan A., Bartels H., Agmon I., Franceschi F., and Yonath A. Structure of functionally activated small ribosomal subunit at 3.3 angstrom resolution. Cell 102 (2000) 615-623
29. Schuwirth B.S., Borovinskaya M.A., Hau C.W., Zhang W., Vila-Sanjurjo A., Holton J.M., and Cate J.H.D. Structures of the bacterial ribosome at 3.5 angstrom resolution. Science 310 (2005) 827-834
30. Wimberly B.T., Brodersen D.E., Clemons W.M., Morgan-Warren R.J., Carter A.P., Vonrhein C., Hartsch T., and Ramakrishnan V. Structure of the 30S ribosomal subunit. Nature 407 (2000) 327-339
31. Yusupov M.M., Yusupova G.Z., Baucom A., Lieberman K., Earnest T.N., Cate J.H.D., and Noller H.F. Crystal structure of the ribosome at 5.5 angstrom resolution. Science 292 (2001) 883-896
32. Zhu J., Penczek P.A., Schröder R., and Frank J. Three-dimensional reconstruction with contrast transfer function correction from energy-filtered cryoelectron micrographs: procedure and application to the 70S Escherichia coli ribosome. J. Mol. Biol. 118 (1997) 197-219